I use SFTP (with SCP) fallback. I need to change the Directory Listing settings, but the section is disabled.
I need to change my File Protocol to "SCP", Directory Listing settings becomes enabled, I change my settings, save, and then change my File Protocol back to "SFTP".

That's deliberate. The option makes sense if you want to use SCP protocol only. And if you want it, you are supposed to select in on login dialog. There's no point selecting "SFTP with SCP fallback", if you want to use SCP only._________________Martin Prikryl

If you need to configure SCP-specific options, it means that you want to use SCP, so you should switch to SCP explicitly.
In other words, if you do not care about protocol, why would you configure protocol specific options?

If SCP specific option are enabled when primary selection is SFTP, it makes user think that SCP options apply to SFTP as well.

And that actually looks like your problem. You seem to try to fix problem with SFTP protocol with options that does not affect it at all.